<div>Purifying the target protein is crucial for investigating its specific properties and interactions with biomolecules like DNA, RNA, and other proteins. A range of purification strategies is available, and the optimal approach depends on factors such as the required scale, throughput, and downstream application. In many cases, the process must be fine-tuned through empirical optimization to achieve the desired purity and yield.</div><div><div><div><div><h3>What is Protein Purification?</h3>Protein purification is a critical process in biotechnology and life sciences, aimed at isolating a specific protein from complex biological mixtures such as cell lysates or tissue extracts. The goal is to obtain a highly purified protein sample, free from contaminants like other proteins, nucleic acids, and lipids, to enable accurate analysis of its structure, function, and interactions.This process is especially vital in biotechnological areas inside immunology and microbiology. In immunology, it underpins the production of vaccines, therapeutic antibodies, and diagnostic assays by enabling the isolation of key immune proteins and antibodies. It also supports the investigation of cell signaling and immune response mechanisms. In microbiology, purified proteins are essential for studying pathogens, identifying disease-related antigens, and driving drug discovery efforts. Ultimately, protein purification is fundamental to the development of targeted vaccines, innovative diagnostics, and effective therapeutic strategies.</div></div></div></div><div><div><div><div><h3>Types of Protein Purification Methods</h3></div></div></div></div><div>There are several types of protein purification methods, each chosen based on the protein’s characteristics such as size, charge, solubility, and binding affinity. Below are some commonly used methods:</div><div><div><div><div><h4>Non-Chromatographic Approaches</h4></div></div><div>Non-chromatographic approaches use simpler physicochemical principles—such as solubility, molecular size, or diffusional properties—to separate and purify proteins. These techniques are often employed as initial purification or concentration steps before further refinement.<h5>Precipitation Techniques</h5>Protein precipitation is a widely used approach in purification workflows, typically relying on one of three main methods:<ul><li>Organic solvent precipitation involves adding solvents like ethanol or acetone to lower the solution's dielectric constant. This promotes protein–protein interactions, reducing solubility and leading to aggregation and precipitation.</li><li>Isoelectric point precipitation exploits the pH at which a protein carries no net charge. At this point, solubility is minimized, causing the protein to precipitate from solution.</li><li>Nonionic polymer precipitation uses polymers such as dextran, polyethylene glycol (PEG), or NPEP to alter the solution’s physical properties. These agents create crowding effects that promote protein aggregation without directly binding to the proteins.</li></ul><h5>Dialysis</h5>Dialysis involves placing a protein solution inside a semi-permeable membrane that allows water and ions to pass while the protein remains inside, facilitating buffer exchange.This method is commonly used during protein expression and purification workflows for buffer exchange, desalting, and removal of unwanted small molecules such as imidazole, urea, or ammonium sulfate. The process helps maintain protein stability and activity by gradually equilibrating the sample with the desired buffer conditions.<h5>Immunocapture (Magnetic Bead-Based Purification</h5>Immunocapture uses antibodies immobilized on solid supports like magnetic beads to selectively bind and isolate a target protein. This method is highly specific and particularly useful for low-abundance targets or small-scale prep, such as:<ul><li>Pulling down proteins from complex mixtures</li><li>Capturing tagged recombinant proteins (e.g., FLAG, HA, or His tags)</li><li>Enrichment before western blotting, MS, or ELISA</li></ul>Magnetic beads offer speed, ease of use, and minimal sample loss, making them ideal for lab-scale workflows.<a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/products/biozenspe-sample-preparation-products/biozen-magbeads">Biozen MagBeads</a> provide a fast and efficient method for purifying, isolating, and cleaning up monoclonal antibodies (mAbs), proteins, and peptides. These paramagnetic beads feature a streptavidin-coated surface, enabling high-affinity binding in immuno-based workflows. Compared to traditional sample preparation techniques, magnetic bead-based immunocapture offers greater speed and consistency by delivering high binding capacity with uniform particle size, ensuring accurate and reproducible results in significantly less time.<h5>Centrifugation</h5>Centrifugation of crude protein mixtures is an essential step in the investigation of protein purification and aggregation. Outlined below are the various types of centrifugations employed in protein purification.Preparative Ultracentrifugation Ultracentrifugation is an effective method of purifying proteins from aggregates based on their size, shape and density. Centrifugation, widely recognized as a robust and versatile method, is commonly used to separate complex mixtures of cellular components. Ultracentrifuges separate small particles by spinning at high speeds, utilizing centrifugal force based on size and density.Differential Centrifugation Differential centrifugation operates by separating components based on differences in size and density, using varying speeds of centrifugation to achieve this. Its resolving power ranges from low to medium. A key advantage of this technique is its convenience for processing multiple samples simultaneously, making it effective for purifying crude samples. Additionally, it preserves cell viability and maintains the natural distribution of hematopoietic cell populations.Rate-zonal Gradient Centrifugation This technique separates components based on their sedimentation rate within a medium that contains a density gradient. It offers medium resolving power and is particularly effective for separating multiple components in complex mixtures with high precision. It is also considered a cost-effective and widely used technique in molecular biology and biochemistry.Isopycnic Centrifugation (Equilibrium Centrifugation) Isopycnic centrifugation is an advanced protein purification method that relies on the principle of separating particles according to their intrinsic buoyant density, irrespective of their size or morphology. During the process, proteins migrate through a density gradient until they equilibrate at a position where their density matches that of the surrounding medium, resulting in precise separation without further sedimentation.</div></div></div><div><div><div><div><h4>Chromatographic Approaches</h4>Chromatography is a common method of protein purification and is based on the separation of molecules in a mixture as they move through a stationary phase and a mobile phase. Outlined below are the various types of chromatography employed in protein purification.<h5>Ion Exchange Chromatography</h5><a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/techniques/hplc-ion-exchange">Ion exchange chromatography</a> relies on the interaction between a charged stationary phase and oppositely charged analytes, with cation exchange chromatography attracting positively charged molecules to a negatively charged stationary phase. Successful application of this technique requires careful selection of the appropriate ion exchange column, buffer pH, and salt concentration. This approach is often used in the biopharmaceutical industries as mAb polishing steps, viral clearance and charge variant analyses as part of the product quality control.<a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/">Phenomenex</a> offers a range of protein purification columns. Their ion exchange chromatography solutions include:&nbsp;<ul><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1526">Luna SCX </a>for strong selectivity of positively charged compounds, such as peptides</li><li><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1540">Biozen WCX</a> for efficient separation of proteins such as monoclonal antibodies charged variants</li><li><a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/part/00g-3151-e0">PhenoSphere SAX</a>, a strong anion-exchanger with fully porous 80Å particles, particularly useful for small molecules such as nucleotides</li></ul><h5>Size Exclusion Chromatography</h5><a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/techniques/hplc-sec">Size exclusion chromatography (SEC)</a> separates molecules based on their size, with larger analytes eluting first due to their exclusion from the pores in the column packing material, while smaller molecules are able to enter the pores, facing a longer travelling path, and hence, eluting later. This method can be categorized into aqueous SEC (gel filtration chromatography, GFC) for analyzing biomolecules such as proteins and antibodies. This type of chromatography is widely used as an analytical tool for quality control in the biopharmaceutical industry and can also be an approach of choice for polishing steps.Phenomenex offers a range of Biozen columns for SEC separations. In the case of mAbs, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1534">Biozen dSEC-2</a> and<a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1537"> Biozen dSEC-7 </a>columns are the top choices for monoclonal antibody (mAb) analysis, delivering high-resolution separation of monomers, aggregates, and fragments formed during mAb manufacturing, processing, or storage. The dSEC-7 column, featuring a larger pore size and optimized particle design, extends the dynamic range to accommodate larger biomolecules and complex biotherapeutics.For more general applications, <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1533">Biozen SEC-2</a> and <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/1532">Biozen SEC-3</a> phases cover different MW ranges for high-efficiency separation of biomolecules (e.g., proteins and antibodies). Additionally, the BioSep and Yarra lines become top choices when looking for preparative scale columns.<h5>Reversed-Phase Chromatography</h5><a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/techniques/hplc-reversed-phase">Reversed-phase chromatography</a>, the most common mode in high-performance liquid chromatography/ ultra-high-performance liquid chromatography (HPLC/UHPLC), separates compounds based on hydrophobic and van der Waals interactions using alkyl (C18, C8, C4) stationary phases or other hydrophobic polymers. For large biomolecules such as proteins and peptides, <a target="_blank" rel="noopener noreferrer" href="https://www.phenomenex.com/resources/blog/wider-pore-biozen-column">wide-pore</a> (typically 300 Å) C4, C8 and C18 columns are ideal, as the larger pore size allows better accessibility of the protein molecules to the stationary phase surface, improving mass transfer and peak shape during separation.The Biozen line from Phenomenex offers a wide range of HPLC/UHPLC columns for the analysis of biomolecules.These include phases optimized for high-resolution analysis of intact proteins (Native-RP, Widepore C4, Intact XB-C8) and peptides (Peptide PS-C18, Peptide XB-C18 and Peptide Polar-C18). Kinetex could also be an option when looking for more selectivities for the analysis of peptides and small proteins. Additionally, when aiming to preparative scale processes, several of these media are also available in Phenomenex Axia formats to easily up-scale your separations.<h5>Hydroxyapatite Chromatography</h5>Hydroxyapatite chromatography (HAC) is a sophisticated mixed-mode chromatographic technique that exploits the unique properties of hydroxyapatite (Ca10(PO4)6(OH)2), utilizing both cation-exchange interactions via its phosphate groups and metal affinity through its calcium sites to achieve highly selective protein separations.Renowned for its efficacy in resolving complex biomolecular separations, HAC excels in tasks like aggregate removal from monoclonal antibodies, surpassing the capabilities of traditional single-mode chromatographic methods such as ion-exchange or hydrophobic interaction chromatography.<h5>Hydrophobic Interaction Chromatography</h5>Hydrophobic interaction chromatography (HIC) is a method of protein purification that separates molecules based on their hydrophobicity, using high-salt buffers to promote protein-ligand interactions while maintaining the protein's biological activity. The process involves gradually reducing the salt concentration to elute proteins in order to increase hydrophobicity, making it effective for purifying target molecules and removing impurities or aggregates, making it a valuable approach for intermediate and polishing steps during purification processes.<h5>Affinity Chromatography</h5>Affinity chromatography is a powerful and highly selective technique used to purify biomolecules based on specific, reversible interactions between a target molecule and an immobilized ligand. In many cases, recombinant proteins are engineered with affinity tags—such as His-tags or GST-tags—that facilitate binding to complementary ligands on the chromatography matrix.This method offers the advantage of achieving several thousand-fold purifications in a single step while preserving the biological activity of the protein. It is widely employed for purifying enzymes, antibodies, and antigens, using a variety of ligands including specific antibodies, enzymes, and multifunctional compounds like concanavalin A and triazine dyes.</div></div></div></div>

Exploring Protein Purification Methods: Essential Techniques for Accurate Results

<h3>A Practical Guide to Getting the Most from Syringe Filters: Tips, Tricks, and Common Pitfalls</h3>Syringe filters play a crucial role in chromatography and many other laboratory applications by removing particulate matter before analysis. Proper sample filtration helps protect analytical instruments, extends column lifetime, and improves data quality. However, selecting an unsuitable filter—or using one incorrectly—can introduce contamination, reduce filtration efficiency, or even compromise analytical results. The following recommendations will help you avoid common mistakes and ensure reliable filtration every time.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_3_150e8c1c2b.webp" alt="KNAUER: Avoiding Common Syringe Filter Mistakes" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_3_150e8c1c2b.webp 133w," sizes="100vw" width="1276" height="1496"><h4>1. Improper Filter Handling</h4>Using excessive force during filtration or attempting to reuse disposable syringe filters can damage the membrane and increase the risk of sample contamination.<ul><li>Solution: Apply slow, even pressure throughout the filtration process and always dispose of single-use filters after one use. If the flow rate decreases noticeably, replace the filter instead of applying additional force.</li></ul><h4>2. Selecting an Inappropriate Pore Size</h4>Using the wrong pore size may either fail to remove unwanted particles or cause the membrane to clog prematurely, reducing filtration efficiency.<ul><li>Solution: A 0.45 µm membrane is generally suitable for routine particulate removal, while a 0.22 µm membrane is recommended for finer filtration and bacterial removal. Samples with higher viscosity may require a pre-filter to prevent rapid clogging. It is also important to consider the intended analytical technique. For example, 0.22 µm filters are typically preferred for UHPLC and LC-MS applications, whereas 0.45 µm filters are often sufficient for conventional HPLC analyses.</li></ul><h4>3. Choosing the Wrong Membrane Material</h4>Different membrane materials exhibit different chemical resistance. Using an incompatible membrane may lead to degradation of the filter, sample contamination, or complete filtration failure.<ul><li>Solution: Always verify solvent compatibility before filtration. PTFE membranes are an excellent choice for organic solvents, while PES and nylon membranes are better suited to aqueous samples. If compatibility is uncertain, perform a small-scale trial before filtering valuable samples.</li><li>Pro Tip: For additional guidance, see our blog article "How to Choose the Right Membrane for your Syringe Filter", which provides a detailed comparison of membrane materials and their recommended applications.</li></ul><img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_2_e47021fb11.jpg" alt="KNAUER Sepapure® Syringe Filters are available with multiple membrane materials, each identified by a dedicated color code for quick and reliable selection." srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_2_e47021fb11.jpg 245w," sizes="100vw" width="1580" height="902"><h4>4. Ignoring Filter Capacity</h4>Using a filter with insufficient capacity can result in rapid membrane blockage, increasing filtration time and reducing laboratory productivity.<ul><li>Solution: When filtering larger sample volumes, choose high-capacity syringe filters or introduce a pre-filtration step. Never force liquid through a clogged membrane, as doing so may damage the filter and negatively affect sample quality.</li></ul><h4>5. Overlooking Sample Adsorption</h4>Certain membrane materials may adsorb analytes of interest, leading to lower recoveries and potentially affecting quantitative results.<ul><li>Solution: For protein samples or other adsorption-sensitive analytes, select membranes with low binding characteristics, such as nylon or glass fiber, whenever appropriate. Performing a small recovery test before routine analysis can help identify potential analyte losses.</li></ul><h4>6. Failing to Optimize Filtration Performance</h4>Slow filtration is more than just an inconvenience—it often indicates that the filtration conditions are not optimal.<ul><li>Solution: If filtration becomes unusually slow, investigate possible causes such as membrane clogging, excessive sample viscosity, or an unnecessarily small pore size. Depending on the sample, dilution or sequential filtration using progressively finer filters may significantly improve performance.</li></ul><h4>Final Thoughts</h4>Selecting the appropriate syringe filter is a straightforward process, but overlooking small details can have a significant impact on analytical performance. Choosing the correct membrane material, pore size, and filtration strategy helps improve laboratory efficiency, protects chromatography systems and columns, and contributes to accurate, reproducible analytical results.With the right syringe filter and proper filtration technique, you can minimize sample preparation problems and maximize confidence in every analysis.<img src="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_4_983a15e289.jpg" alt="KNAUER: Sepapure® Syringe Filter Selection" srcset="https://storage.googleapis.com/labrulez-bucket-strapi-h3hsga3/thumbnail_KNAUER_Avoiding_Common_Syringe_Filter_Mistakes_4_983a15e289.jpg 245w," sizes="100vw" width="1160" height="627">Happy filtering!

Avoiding Common Syringe Filter Mistakes

News from LabRulezLCMS Library - Week 27, 2026

Article

Product

Application

Academy

Poster

Everything from the world of analytical chemistry in one place. We connect people in solving their problems. At Labrulez you will find all the necessary information easily, quickly and clearly. Stop searching and start finding.

LabRulez

Phenomenex is a global technology leader committed to developing novel analytical chemistry solutions that solve the separation and purification challenges of researchers in industrial, government and academic laboratories.

Phenomenex

Based in Berlin, KNAUER is a medium-sized, owner-managed company that has been serving the sciences since 1962. We develop and manufacture scientific instruments of superior quality for liquid chromatography, including: Analytical HPLC/UHPLC, Preparative HPLC, Fast protein liquid chromatography (FPLC), Multi-column chromatography/Simulated moving bed (SMB) chromatography. High pressure dosing, in-line detection systems, and osmometry are additional business areas.

KNAUER

New Food magazine

Agilent Technologies

Thermo Fisher Scientific

SelectScience

Evosep Biosystems

A novel spatial technique, DISCO-MS, combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry with the Bruker timsTOF instrument family. This combination enables DISCO-MS to perform unbiased proteome analysis of preclinical and clinical tissues from quantity-limited materials after unbiased imaging of entire specimens in 3D.
In this webinar, you will learn about a new experimental approach that combines whole tissue clearing, dia-PASEF®, and trapped ion mobility spectrometry (TIMS) mass spectrometry to analyze the spatial proteome of complex tissue structures. The webinar will detail how with this technique, researchers were able to:
<ul>
<li>Analyze the proteome of preclinical and clinical tissues after identification of regions of interest using 3D imaging, followed by robotic tissue extraction</li>
<li>Achieve early unbiased detection and characterization of subtle tissue perturbations across pathologies</li>
<li>Benefit from the use of ultra-high sensitivity and robust timsTOF mass spectrometers</li>
</ul>
<h5>Key learning objectives</h5>
<ul>
<li>Discover the new experimental approach that combines whole tissue clearing, dia-PASEF®, and TIMS mass spectrometers can be used to analyze the spatial proteome of complex tissue structures</li>
<li>Understand how researchers were able to analyze the proteome of specific tissue regions following 3D imaging to enable robotic tissue extraction</li>
<li>Learn about the unparalleled sensitivity and robustness the timsTOF platform offers with 4D-Proteomics™ which enables researchers to delve deeper into proteome analysis and gain greater insights</li>
</ul>
<blockquote>
Presenter: Dr. Harsharan Singh Bhatia (Institute for Tissue Engineering and Regenerative Medicine (iTERM))
</blockquote>
<blockquote>
Dr. Harsharan Singh Bhatia is the Omics technologies team leader at the Institute for Tissue Engineering and Regenerative Medicine (iTERM), Helmholtz Munich. He completed his Ph.D. at the University of Freiburg, Germany, studying the neuroprotective role of dietary antioxidants. Bhatia worked as a postdoctoral researcher at UCLA, where he investigated the impact of dietary manipulations on rodent behavior. He later returned to the University of Freiburg to work as a research associate at the University Clinic, exploring epigenetic factors&#39; regulation of microglial function. In 2017, Bhatia joined iTERM to study chronic neuroinflammation using DISCO tissue clearing and spatial-omics tools.
</blockquote>
<blockquote>
Presenter: Jemima Arnold (Editorial Team, SelectScience)
</blockquote>
<blockquote>
Jemima studied Cellular and Molecular Medicine at the University of Bristol, UK, and as a member of the Editorial team, she now plays an integral role in shaping the content on SelectScience.
</blockquote>

SelectScience: Spatial proteomics in three-dimensional intact specimens

Spatial proteomics in three-dimensional intact specimens

A new experimental approach that combines whole tissue clearing, dia-PASEF®, and TIMS MS to analyze the spatial proteome of complex tissue structures.

TBD
<blockquote>
Presenter: Mark Sartain, Ph.D. (LC/MS Applications Scientist, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Mark has developed a diverse array of targeted and nontargeted mass-spectrometry based metabolomics and lipidomics applications since joining Agilent in 2012, with a focus on complete hardware/software workflows. Mark began utilizing mass spectrometry in his graduate work to characterize glycoproteins, and later established a novel LC/MS strategy to comprehensively profile and identify complex lipids of Mycobacterium tuberculosis in his postdoctoral fellowship at Colorado State University. He continued designing a wide range of MS-based techniques to measure metabolites and lipids for diverse projects as a Research Scientist at the Institute of Systems Biology (Seattle, WA) prior to joining Agilent.
</blockquote>

Agilent Technologies: LC/TQ Solutions to Give Your Lab Multi-omic Biological Insights

LC/TQ Solutions to Give Your Lab Multi-omic Biological Insights

LC/TQ to Give Your Lab Multi-omic Biological Insights

TBD
<blockquote>
Presenter: Mark Sartain, Ph.D. (LC/MS Applications Scientist, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Mark has developed a diverse array of targeted and nontargeted mass-spectrometry based metabolomics and lipidomics applications since joining Agilent in 2012, with a focus on complete hardware/software workflows. Mark began utilizing mass spectrometry in his graduate work to characterize glycoproteins, and later established a novel LC/MS strategy to comprehensively profile and identify complex lipids of Mycobacterium tuberculosis in his postdoctoral fellowship at Colorado State University. He continued designing a wide range of MS-based techniques to measure metabolites and lipids for diverse projects as a Research Scientist at the Institute of Systems Biology (Seattle, WA) prior to joining Agilent.
</blockquote>

Agilent Technologies: Elucidating Cellular Metabolism with a Full Suite of Next-Generation Omics Tools

Elucidating Cellular Metabolism with a Full Suite of Next-Generation Omics Tools

Cellular Metabolism with a Next-Generation Omics Tools

Join this webinar to hear from Dr Lin Qingsong, Principle Research Fellow, Director, Protein and Proteomics Centre, National University of Singapore and be informed about up-to-date risk assessment considerations of alternative proteins.
About this webinar
Alternative proteins are gaining momentum as a viable and sustainable option to traditional animal-based proteins. In this webinar, we will focus on the applications and potential of omics in key research areas, which drive innovation and food safety in alternative proteins.
Learning points:
<ul>
<li>Be informed about up-to-date risk assessment considerations of alternative proteins</li>
<li>Understand how multi-omics can study novel foods (alternative proteins)</li>
<li>Understand how omics output can help in improving and creating new food safety guidelines to ensure safe alternative proteins for consumers</li>
</ul>
Technical highlights:
<ul>
<li>Protein extraction and proteomics digestion considerations for alternative protein samples</li>
<li>Data processing and databases for discovery proteomics in novel foods</li>
</ul>
<blockquote>
Presenter: Dr Lin Qingsong (Principal Research Fellow (Research Associate Professor), Director, Protein and Proteomics Centre)
</blockquote>
<blockquote>
<ul>
<li>2002 PhD University of Toronto, Canada (major in Clinical Biochemistry)</li>
<li>1994 MSc Xiamen University, China (major in Enzymology)</li>
<li>1991 BSC Xiamen University, China (major in Biochemistry)</li>
</ul>
</blockquote>
<blockquote>
Proteomics and mass spectrometry, Cancer biomarker discovery and cancer biology, Chemical proteomics and drug target identification, Mechanisms of water desalination in mangrove plants and euryhaline fish, Aquaporin biomimetic membrane for water desalination and reuse.
</blockquote>

SCIEX: Omics in the rapidly developing field of alternative proteins: innovation and safety

Omics in the rapidly developing field of alternative proteins: innovation and safety

Join this webinar and be informed about up-to-date risk assessment considerations of alternative proteins.

Omics in developing field of alternative proteins

L-asparaginase (ASNase) is an enzyme-drug that is approved for the treatment of pediatric acute lymphoblastic leukemia (ALL) but is too toxic for adults. To elucidate potentially targetable mechanisms of toxicity with the ultimate goal of decreasing ASNase toxicity and extending its use to adults, we performed multi-omic profiling of the response to ASNase in adult (16-week-old) mice. We administered a range of sub-toxic and toxic doses of ASNase to healthy mice, collected whole blood samples, processed them to plasma, and used a novel sample preparation with just 20 µL mouse plasma as input. We analyzed the extracts using a multi-omic, bioanalytical LC/MS platform capable of measuring 500+ metabolites, 750+ lipids, and 375 peptides.
A Bio-LC was used with three different separations for metabolites, lipids, and peptides. A fast, sensitive, robust, 6495 LC/TQ MS system was used with comprehensive databases for pathway analysis. The results suggested that ASNase induces multi-modal cell death as evidenced by metabolite-, lipid-, and peptide/protein-level changes that occurred in a dose-dependent manner. 
Future studies will test the hypothesis that inhibiting those modes of cell death will decrease ASNase toxicity while preserving anticancer activity. Overall, our findings provide proof-of-concept that multi-omic analysis of drug mechanisms at the protein-, lipid-, and metabolite-levels can unveil toxicity-associated pathways that can be targeted to potentially improve a drug’s therapeutic index.
<blockquote>
Presenter: Ian Edwards (LC/TQ Product Manager, Agilent Technologies, Inc.)
</blockquote>
<blockquote>
Ian holds a Ph.D. from the Centre for Proteome Research at the University of Liverpool.He has spent time as a pre- and post-sales MS applications specialist focused on MS imaging and proteomics, as a field marketing manager for -omics, and as a global pharmaceutical marketing manager. Ian joined Agilent recently as LC/TQ Product Manager.
</blockquote>
<blockquote>
Presenter: Philip Lorenzi, Ph.D. (Associate Professor, Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center)
</blockquote>
<blockquote>
I’m an Associate Professor in the Department of Bioinformatics and Computational Biology at The University of Texas MD Anderson Cancer Center. My laboratory focuses on the development of metabolic therapies for the treatment of cancer (with an emphasis on nutrient metabolism), and I’m also Director of the Proteomics Core Facility and Director of the Metabolomics Core Facility. I’ve co-authored 71 peer-reviewed publications. I co-wrote and was Co-Investigator on a successfully completed $4.5M CPRIT Core Facility Award, managed staff and the budget, and oversaw development of bioanalytical services using current equipment and protocols that we have optimized thoroughly. We’ve developed novel mass spectrometry-based methods for: 1) increasing the accuracy of glutamine and glutamate measurements by minimizing in-source conversion to pyroglutamate; 2) normalizing data based on the DNA content of cell- and tissue-based samples; 3) measuring amino acids from as little as 2 µL of mouse plasma or whole blood; 4) detection of over 2,000 annotated metabolites and lipids per biological sample (including just 2 mg of tissue); 5) stable isotope tracer analyses in vitro and in vivo including methods for measuring energy metabolism; 6) determining the extent and position of 13C incorporation into specific amino acids; and 7) diagnosing and correcting batch effects in metabolomic data. Our multidisciplinary team provides full service contract research in a state-of-the art facility.
</blockquote>

Agilent Technologies: Multi-Omic, Mass Spectrometry-Based Elucidation of Mech. of L-asparaginase Toxicity in a Mouse Model

Multi-Omic, Mass Spectrometry-Based Elucidation of Mech. of L-asparaginase Toxicity in a Mouse Model

We analyzed the extracts using a multi-omic, bioanalytical LC/MS platform capable of measuring 500+ metabolites, 750+ lipids, and 375 peptides.

Multi-Omic, Mass Spectrometry-Based Elucidation of Mech

It’s an exciting time to be a proteomics researcher without a doubt. For years the biggest challenge has been the sheer volume of samples to be analysed. The recent launch of the Thermo Scientific™ Orbitrap™ Astral™ mass spectrometer has promised to be a true game-changer.
For the first time ever, an instrument is available which offers the capability to do high throughput studies of large cohort samples without compromising performance. Join us for this review of presentations from the recent BSPR-EuPA conference showcasing the latest innovations.
Learning points:
<ul>
<li>Latest advances in high throughput proteomics
</li>
<li>Latest advances in large cohort analysis
</li>
<li>Revolutionary instrumentation for deeper proteome coverage
</li>
</ul>
Who should attend:
<ul>
<li>Director, Managers and Researchers in Proteomics
</li>
<li>Director, Managers and Researchers in Cancer Research facilities
</li>
<li>Current users of Orbitrap technology &amp; QTOF MS analysing plasma proteins
</li>
</ul>
<blockquote>
Presenter: Prof Michael MacCoss (Director of MacCoss Lab, University of Washington, Department of Genome Sciences)
</blockquote>
<blockquote>
Michael J MacCoss was born in western Canada to British parents, before relocating to Freehold, New Jersey where he grew up. Mike attended the University of Vermont as an undergrad, receiving a Bachelor of Arts in Chemistry. However, his passion for research only truly came to be after an internship in Dr. Patrick Griffin’s protein mass spectrometry lab at Merck Research Laboratories, and he began pursuing a path in biotechnology.
</blockquote>
<blockquote>
Eventually, Mike obtained a Ph.D. with Professor Dwight Matthews, also at the University of Vermont, and followed that with a post-doc at Scripps Research Institute with Professor John R. Yates III. In 2004 he started the MacCoss lab at the University of Washington with a major emphasis on developing robust and quantitative protein assays.
</blockquote>
<blockquote>
Over the last 14 years, Mike and his team have become leaders in the field of quantitative proteomics. The focus of his lab is the development of methods and software for generating and disseminating quantitative protein assays.
</blockquote>
<blockquote>
Presenter: Dr. Jo Kirkpatrick (Senior Product Specilaist, Thermo Fisher Scientific)
</blockquote>
<blockquote>
Jo has a degree in Chemistry from the University of York and a PhD in analytical chemistry from the University of Reading. Following a post-doc in mass spectrometry in the Chemistry department at Oxford, and working as an application scientist at Waters, she has worked in and ran Proteomics Core Facilities in the UK and Germany, including the EMBL in Heidelberg, the Leibniz Institute on Aging in Jena, The Francis Crick Institute in London and CRUK Cambridge.
</blockquote>
<blockquote>
After many years as an experienced Thermo customer, Jo joined the company earlier this year as a Technical Sales Specialist, supporting the whole of the UK/Ireland, Benelux and Nordic regions, in all things proteomics.
</blockquote>
<blockquote>
When she&#39;s not talking about proteomics and mass spectrometry, Jo enjoys ceroc dancing, tennis, scuba diving, travelling, and spending time with her cats, who like to join in on Teams meetings whenever she works from home.
</blockquote>
<blockquote>
Presenter: Dr. Paul Humphrey (EMEA Senior Regional Marketing Manager, LSMS, Omics and ClinTox, Thermo Fisher Scientific)
</blockquote>
<blockquote>
Paul has a degree in Analytical Chemistry and a PhD in Secondary Ion Mass Spectrometry from the University of Manchester.
</blockquote>
<blockquote>
He previously managed a contract analysis laboratory for several years before moving into a career in the scientific instrument manufacturing industry.
</blockquote>
<blockquote>
Initially an application chemist and product manager he moved into international scientific marketing when he joined Thermo Fisher Scientific in 1997. Since then he has worked in a variety of roles within factory, field marketing and sales office organisations. He has travelled and presented extensively and has been responsible for business in EMEA, North America and Asia/Pacific regions.
</blockquote>
<blockquote>
He lives in the UK and when not working he enjoys travelling, photography, cookery and scuba-diving.
</blockquote>
<blockquote>
Presenter: Robert van Ling (Product Manager, Thermo Fisher Scientific)
</blockquote>
<blockquote>
Robert started his low flow chromatography career as an intern from the Technical School in Amsterdam, The Netherlands, at LC Packings in the mid-90s.
</blockquote>
<blockquote>
Since those early years, Robert has been part of the teams introducing and supporting a wide range of our nano- and capLC products, such as the UltiMate and UltiMate 3000 nanoLC systems, PepMap and EASY-Spray columns. In recent years, he has introduced our new µPAC Neo HPLC column line, an innovative and unique approach to significantly improve the performance and reliability in low flow proteomic separations.
</blockquote>
<blockquote>
Robert still lives in the wider Amsterdam region, and when not talking low flow separations very much enjoys reading fantasy, jigsaw puzzling and listening to prog and hard rock.
 
</blockquote>

Thermo Scientific: Proteomics unleashed: exclusive insights and updates from BSPR-EuPA

Proteomics unleashed: exclusive insights and updates from BSPR-EuPA

Review of presentations from the recent BSPR-EuPA conference showcasing the latest innovations.

Exclusive insights and updates from BSPR-EuPA

Immunopeptidomics is an emerging field that combines proteomics and immunology to study the complex repertoire of peptides presented by major histocompatibility complex (MHC) molecules on the cell surface.
These MHC-bound peptides, known as immunopeptidomes, play crucial roles in immune recognition and activation, influencing various physiological and pathological processes such as immune surveillance, infectious diseases, autoimmunity, and cancer.
Join our webinar to explore recent advancements, challenges, and applications in immunopeptidomics. Discover how Evosep One accelerates discoveries, and support the understanding of immune responses and diseases.
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Presenter: Anthony Purcell (Professor, Purcell Lab, Monsah University)
</blockquote>
<blockquote>
Presenter: Nicolai Bache (Head of Applications at Evosep)
</blockquote>

Advancing Immunopeptidomics

Recent advancements, challenges, and applications in immunopeptidomics.

Immunopeptidomics is a field that combines proteomics and immunology to study the complex repertoire of peptides presented by major histocompatibility complex (MHC) molecules on the cell surface.
These MHC-bound peptides, known as immunopeptidomes, play crucial roles in immune recognition and activation, influencing various physiological and pathological processes such as immune surveillance, infectious diseases, autoimmunity, and cancer.
Join our webinar to explore recent advancements, challenges, and applications in immunopeptidomics. Discover how EvosepOne accelerates discoveries, and support the understanding of immune responses and diseases.
<h4>IMMUNOPEPTIDOMICS ON THE EVOSEP ONE – NEW LEVELS OF SAMPLE THROUGHPUT AND PRODUCTIVITY</h4>
Immunopeptidomics is the study of peptide antigens that are bound to and presented on the cell surface by molecules encoded by the Major Histocompatibility, a highly polymorphic region of the genome that encode molecules involved in immune responses. These peptides are derived from both intracellular and extracellular degradation of the parental proteins, generating a highly complex repertoire of peptide ligands, including peptides derived from pathogens, tissue specific and cancer specific antigens when relevant. In humans, human leukocyte antigen (HLA) class I and class II molecules are of particular interest for immunopeptidomic analysis. These molecules are encoded by several loci and constitute thousands different alleles that vary between individuals. Thus, immunopeptidomes are highly individualized and almost impossible to accurately predict. This predicates the empirical measurement of the complexity and diversity of immunopeptidomes using mass spectrometry. Due to the relatively small amounts of material available for analysis the use of nanoflow LC-MS for immunopeptidome analysis is critical. Here I explore the implementation of the high throughput EvoSEP one platform couples to a Bruker timsTOF Pro 2 for robust analysis of immunopeptidomes across a variety of tissues and cell lines. Using the Whisper 20SPD method data quality and depth is maintained whilst sample carryover is negligible allowing more productive use of instrument time; I highlight significant improvements in throughput with over 1500 immunopeptidomes characterised in just 3 months.
<blockquote>
Presenter: Anthony Purcell (Professor, Purcel Lab, Monsah University)
</blockquote>
<blockquote>
Presenter: Nicolai Bache (Head of Applications at Evosep)
</blockquote>
<h4>MAPPS: High throughput immunopeptidomics for the assessment of the immunogenic potential of protein biotherapeutics</h4>
Biologics, mostly monoclonal antibodies and recombinant proteins, are a class of drugs used to treat some particularly difficult conditions. These proteins, when recognized as non-self by the immune system, can elicit unwanted immunogenicity. One of the first steps in this cascade is the presentation of fragments of this protein by MHC complexes on antigen presenting cells, which might ultimately lead to generation of anti-drug antibodies (ADAs). These ADAs can lower the therapeutic efficiency and can lead to severe immunogenic effects. To bring safe biotherapeutics to the market it is critical to thoroughly assess the immunogenic profile of a biotherapeutic. MAPPS (MHC associated peptides proteomics) assays are the method of choice to define all potential immunogenic regions of a protein. ImmuneSpec, an advanced immunopeptidomics platform, offers MAPPS as a service. Here we show how the combination of high-throughput MHC peptide purification, fast LC using EvoSep, and high sensitive MS addresses these needs.
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Presenter: Kurt Boonen (Assistant Professor, Deparment of biomedical sciences, University of Antwerp)
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Presenter: Nicolai Bache (Head of Applications at Evosep)
</blockquote>

Evosep: ADVANCING IMMUNOPEPTIDOMICS: LEVERAGING EVOSEP ONE FOR HIGH-THROUGHPUT ANALYSIS AND DISCOVERY

ADVANCING IMMUNOPEPTIDOMICS: LEVERAGING EVOSEP ONE FOR HIGH-THROUGHPUT ANALYSIS AND DISCOVERY

Immunopeptidomics: HIGH-THROUGHPUT ANALYSIS AND DISCOVERY

Lipidomics is a subset of metabolomics, focused specifically on the analysis of lipid species.
Lipids are among the most vital compounds in living organisms that serve to fulfil various functions, including building blocks for cellular and extracellular vesicle membranes, cell signaling, and energy storage. Studying the biological function of lipids plays a significant factor in understanding their overall effect on human health.
 The structure of a lipid can be altered, due to a shift in their environment caused by endogenous or exogenous factors. These factors can be genetics, diet-base, or caused by diseases. The classes of lipids vary in polarity, from phospholipids to triacyl glycerides, and it is estimated that there are over 300,000 possible lipid structures with varying fatty acyl chain lengths from 12 to 26 carbons. Mass spectrometry (MS)-based lipidomics generally require the use of liquid chromatography to separate the complex lipids present in biofluids, based on polarity and high-resolution MS to accurately measure the mass-to-charge (m/z).
 Join Dr. Timothy Garrett, Associate Professor at the University of Florida, to find out more about the technology needed for the correct identification of lipids, and how monodisperse particles can improve the speed and separation capacity of lipids. Plus, Garrett will also explore the analytical advances in chromatography and bioinformatics (IE-Omics), in the context of several disorders, including malaria, cancer and rare diseases.
Key learning objectives
<ul>
<li>Learn the basics of applied lipidomics using ultra-high-performance liquid chromatography- high-resolution mass spectrometry (UHPLC-HRMS/MS)
</li>
<li>Understand how lipidomics can be used for developing new diagnostic tests
</li>
<li>Discover the potential of lipidomics, while understanding current limitations
</li>
<li>Understand the role of chromatography in lipidomics
</li>
<li>Learn how utilizing monodisperse fully porous particles can improve your current lipidomics method
</li>
</ul>
Who should attend?
<ul>
<li>LC scientists that are looking for more lipidomic separations efficiency
</li>
<li>Scientists looking to improve their current HPLC/UHPLC separations for metabolomics
</li>
<li>Chromatographers looking to start developing new lipidomics based HPLC/UHPLC methods
</li>
</ul>
<blockquote>
Presenter: Timothy J. Garrett (Associate Professor, University of Florida, View Biography)
</blockquote>
<blockquote>
Dr. Timothy J. Garrett is an Associate Professor and Chief of Experimental Pathology in the Department of Pathology, Immunology and Laboratory Medicine at the College of Medicine, University of Florida. Garrett has also served as PI or Co-PI on grants and contracts totaling over $39M of funding from institutions such as the National Institutes of Health (NIH), Juvenile Diabetes Research Foundation (JDRF) and the American Diabetes Association (ADA). He has an undergraduate degree and a PhD in Chemistry. As a graduate student, he worked on the development and design the first imaging mass spectrometry ion trap instrument through a partnership with Thermo Fisher Scientific and studied the disposition and characterization of phospholipids in brain tissue. He has over 20 years of experience working with Thermo Fisher Scientific instrumentation including the TSQ 7000. He joined the faculty at the University of Florida in 2006, where he has developed a research program in metabolomics, lipidomics, and small molecule quantitation for clinical and biological research using mass spectrometry approaches. He is also currently Co-Editor-in-Chief for the Journal of Mass Spectrometry and Advances in the Clinical lab.
</blockquote>
<blockquote>
Presenter: Carrie Haslam (SelectScience)
</blockquote>
<blockquote>
Dr. Carrie Haslam is an Associate Editor at SelectScience, playing a key role in content production and specializing in Materials Science, Alzheimer’s disease and Clinical Diagnostics. Carrie completed a Ph.D. from The University of Plymouth, where she developed graphene-based biosensors for the early diagnosis of Alzheimer’s disease.
</blockquote>

SelectScience: Mass spectrometry-based lipodomics using monodisperse particle UHPLC/HPLC (MFPP) columns for biomarker discovery

Mass spectrometry-based lipodomics using monodisperse particle UHPLC/HPLC (MFPP) columns for biomarker discovery

Technology needed for the correct identification of lipids, and how monodisperse particles can improve the speed and separation capacity of lipids.

Mass spectrometry-based lipodomics & MFPP columns

Learn how you can achieve confident, sensitive and reproducible AAV HCP identification.
This webinar will demonstrate approaches to overcome key challenges with AAV HCP analysis, such as the highly complex proteome background and large dynamic range which necessitate the need for high sensitivity enabling the detection and quantification of low abundant HCPs, essential for safe and efficacious production of these advanced biotherapeutics.
<h5>In this webinar you’ll learn:</h5>
<ul>
<li>How to overcome challenges in HCP analysis of AAV based gene therapies</li>
<li>How to ensure you accurately profile and quantify critical HCP contaminants in the sub ppm range</li>
<li>How the new <a href="https://lcms.cz/products/836">Thermo Scientific Orbitrap Astral Mass Spectrometer</a> can aid your HCP analysis</li>
</ul>
<blockquote>
Presenter: (Jonathan Bones, Principal Investigator, Characterization and Comparability Group, NIBRT)
</blockquote>
<blockquote>
Professor Bones obtained his BS in Analytical Science (Chemistry) and PhD in Analytical Chemistry from Dublin City University (DCU). Jonathan joined Prof. Pauline M. Rudds group at NIBRT in 2007.
</blockquote>

Chromatography & Mass Spectrometry: Host Cell Protein (HCP) Profiling and Quantitation in Gene Therapy Products with the Orbitrap Astral Mass Spectrometer

Host Cell Protein (HCP) Profiling and Quantitation in Gene Therapy Products with the Orbitrap Astral Mass Spectrometer

This webinar will demonstrate approaches to overcome key challenges with AAV HCP analysis.

LCMS webinars focusing on OMICS - page 20